Here are a few I can think of that have two levels of track.
Secaucus, NJ, Amtrak, NJT on NEC on top and NJT on the bottom.
https://maps.google.com/maps?hl=en&ll=40.761131,-74.075433&spn=0.002186,0.003471&t=h&z=19
Newark, NJ Amtrak, NJT on NEC on lower level and Path on upper level...